Contacts of the strand formed by residues 100 - 106 (chain B) in PDB entry 2VTX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B PHE 4.0 1.0 - - - +
31B GLU* 3.7 1.1 - - - -
32B PHE* 3.0 43.4 + - + +
45B LEU* 4.9 4.9 - - + -
65B ILE* 4.1 18.6 - - + -
66B VAL 5.4 0.7 - - - +
96B LEU* 3.8 43.1 - - + -
97B ASP 3.7 14.4 - - - +
98B PRO* 3.9 8.3 - - + -
99B PRO* 1.3 78.0 - - - +
101B THR* 1.3 63.6 + - - +
102B PHE* 4.1 19.1 + - + -
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR* 3.4 33.0 - - + -
30B PHE 3.8 2.9 - - - +
31B GLU* 3.2 27.4 + - + +
65B ILE* 3.3 5.2 - - - +
66B VAL* 2.6 63.5 + - + -
99B PRO 4.5 0.2 + - - -
100B VAL* 1.3 74.8 - - - +
102B PHE* 1.3 66.3 + - - +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TRP* 3.6 28.3 - + - -
21B CYS* 4.5 4.0 - - - -
23B LEU* 4.2 9.3 - - + +
28B LYS 4.0 0.3 - - - +
29B THR* 3.5 1.2 - - - -
30B PHE* 3.0 41.4 + + - +
32B PHE* 4.6 1.6 - - + -
45B LEU* 4.2 10.5 - - + -
47B LEU* 4.0 37.0 - - + -
63B VAL* 4.7 6.3 - - + -
64B GLU 3.4 4.7 - - - +
65B ILE* 4.1 25.4 - - + -
78B ILE* 4.9 1.3 - - + -
96B LEU* 4.2 4.0 - - + -
100B VAL* 4.1 23.3 - - + -
101B THR* 1.3 74.8 - - - +
103B ARG* 1.3 63.5 + - - +
113B ILE* 3.8 28.5 - - + -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.0 5.8 - - - +
28B LYS* 3.4 9.9 - - + +
29B THR* 3.4 24.7 + - + +
63B VAL* 3.3 2.6 - - - -
64B GLU* 2.7 64.1 + - + +
66B VAL* 3.6 26.7 - - + +
73B GLU* 3.5 35.0 + - - -
75B SER* 3.6 13.9 + - - -
102B PHE* 1.3 75.8 - - - +
104B LEU* 1.3 73.3 + - - +
105B LYS* 3.2 7.4 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 4.0 14.8 - - + +
24B ASN* 3.9 34.3 - - - +
25B GLU* 5.0 0.7 - - - -
28B LYS* 2.9 40.0 + - + +
61B HIS* 4.5 3.1 - - + -
62B ILE 3.6 9.9 - - - +
63B VAL 4.8 0.2 - - - +
103B ARG* 1.3 73.3 - - - +
105B LYS* 1.3 66.0 + - - +
106B ALA* 3.2 25.1 + - - +
107B GLY 3.2 24.7 - - - +
109B GLY* 4.1 6.5 - - - +
111B LEU* 3.7 32.1 - - + -
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 5.9 2.2 - - - -
112A TYR* 3.7 27.1 + - - -
62B ILE* 2.9 36.6 + - + +
64B GLU* 3.3 40.3 + - + +
75B SER* 5.3 1.0 + - - -
77B PRO* 4.3 9.6 - - + +
103B ARG* 3.2 5.8 + - - +
104B LEU* 1.3 74.5 - - - +
106B ALA* 1.3 59.1 + - + +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.7 26.5 - - - +
60B PHE 3.8 10.8 - - - +
61B HIS* 3.3 2.3 - - - -
62B ILE* 3.1 39.9 + - + -
104B LEU* 3.2 12.8 + - - +
105B LYS* 1.3 80.5 - - + +
107B GLY* 1.3 62.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il